Polkinghorne received an additional doctorate in theoretical elementary particle physics from Trinity College in 1974. His creation of mathematical models to calculate the paths of quantum particles was recognized that year with his selection as a fellow of the Royal Society. Five years later Polkinghorne concluded that his research had come to an end. To the surprise of many colleagues, he resigned his post and began theological studies at Westcott House in Cambridge. He was ordained in 1982 and assigned to a parish in South Bristol. He became vicar of a parish in Blean in 1984 and two years later was appointed fellow, dean, and chaplain of Trinity Hall, Cambridge. In 1989 he was appointed president of Queens’ College, Cambridge, from which he retired in 1996.

In 1983 Polkinghorne published The Way the World Is, in which he explained how a thinking person can be a Christian. It was the first of several works on the relationship between science and religion. The Faith of a Physicist: Reflections of a Bottom-Up Thinker appeared in 1994 and Faith, Science and Understanding in 2000. Later publications exploring this fraught territory were The God of Hope and the End of the World (2002), Science and the Trinity: The Christian Encounter with Reality (2004), and Quantum Physics and Theology: An Unexpected Kinship (2007). He published an autobiography, From Physicist to Priest, in 2007.

In 1986 Polkinghorne helped found the Society of Ordained Scientists, a preaching order of the Anglican Communion, and he was founding president (2002–04) of the International Society for Science and Religion. He was also a member of the Science Research Council (1975), the Doctrine Commission of the Church of England (1989–95), and the Human Genetics Advisory Commission (1999–2002). Polkinghorne was knighted by Queen Elizabeth II in 1997 for distinguished service to science, religion, learning, and medical ethics. He was awarded the 2002 Templeton Prize for Progress Toward Research or Discoveries About Spiritual Realities.

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